Intersection of the DEA result

There are more differentially expressed transcripts detected between the treated and untreated conditions using the paired-end protocol. The paired-end protocol allows us to obtain both homogeneous samples and more biological information, as shown in the Kallisto output.

Furthermore, when a PCA is performed with the paired-end protocol, 97% of the dataset’s variability is explained by the treated/untreated feature, compared to 89% for the single-end protocol. This indicates that the biological variability of primary interest (the treatment effect) is much more highlighted and manageable with the paired-end protocol.

Due to the clarity and uniformity of the variability explained by the treatment condition in the paired-end protocol, the DEA results become more meaningful and easier to exploit. This may also explain why a greater number of differentially expressed transcripts are identified.

The paired-end protocol provides more biological information, which in turn offers greater statistical power, higher confidence in the results, and a clearer signal of the treatment effect compared to the single-end protocol.

Conversely, the single-end protocol introduces more noise into the results, making it less suitable for this type of analysis.

In conclusion, there is a clear treatment effect on the sequenced individuals, regardless of the protocol used. However, this effect is better highlighted when the paired-end protocol is employed.

Multivariate model (EXPERIMENTAL)